Zhao Xueyan, Zhao Kewei, Ren Jun, Zhang Feng, Jiang Chao, Hong Yuan, Jiang Kai, Yang Qiang, Wang Chengbin, Ding Nengshui, Huang Lusheng, Zhang Zhiyan, Xing Yuyun
Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
Anim Sci J. 2016 May;87(5):646-54. doi: 10.1111/asj.12468. Epub 2015 Oct 1.
Boar reproductive traits are economically important for the pig industry. Here we conducted a genome-wide association study (GWAS) for 13 reproductive traits measured on 205 F2 boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F2 intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome-wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r(2) correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.
公猪的繁殖性状对养猪业具有重要经济意义。在此，我们针对在205头F2代公猪300日龄时测量的13个繁殖性状进行了全基因组关联研究（GWAS），使用了从1200头猪的参考群体中推算出的60K单核苷酸多态性（SNP）数据，该参考群体来自大白杜洛克×二花脸F2代杂交群体。我们在8条猪染色体（SSC）上鉴定出了与7个性状相关的10个显著位点。两个位点超过了全基因组显著性水平，其中一个位于SSC7上约60.25 Mb处，与附睾重量有关；另一个位于SSC4上约43.69 Mb处，与精液温度有关。我们鉴定出的10个显著位点中有4个与先前报道的公猪繁殖性状数量性状位点一致。我们在这些位点突出了几个有趣的候选基因，包括APN、TEP1、PARP2、SPINK1和PDE1C。为了评估推算准确性，我们使用PCR限制性片段长度多态性或桑格测序法对9个GWAS顶级SNP进行了进一步基因分型。我们发现推算基因型数据与真实基因型数据之间的基因型一致性平均为91.44%，等位基因一致性为95.36%，r(2)相关性为0.85。这表明我们基于推算SNP数据的GWAS定位结果是可靠的，为深入了解公猪繁殖性状的遗传基础提供了依据。
